Merge branch 'master' into add_sga_step
Revert "Add ability to accept one shuffled fastq file for preprocessing"

This reverts commit 77116c14a5a7cfe39075ca1f3a7a8be9095b0487.
Make -d default value 1000000
Make default indexing algorithm ropebwt
Make -d default 1000000 and algorithm ropebwt
Do not need to use -d option as we use the ropebwt indexing algorithm
Accept one interleaved fastq file
Adjust parameters to reflect the preprocessing of one fastq file, default algorith ropebwt and no -d disk value
Test if SGA code can handle a single interleaved fastq file
Edited to handle a single interleaved fastq file in addition to separate forward and reverse files
Corrected wrong variable name and added missing brackets.
Fixed extra brackets
Only move the results file if it exists
Do not zip SGA corrected file by default
Minor change to comments
Minor changes to getting the cwd at start of script
Get absolute paths of the input files
Zip file only if user has specified a zipped output filename
Comments added to show that the results will only be zipped if user specifies a zipped output filename
Comments added about optional zipping of output